NM_001034853.2(RPGR):c.1217dup (p.Ser407fs) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jun 13, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001008566.22

Allele description [Variation Report for NM_001034853.2(RPGR):c.1217dup (p.Ser407fs)]

NM_001034853.2(RPGR):c.1217dup (p.Ser407fs)

Gene:

RPGR:retinitis pigmentosa GTPase regulator [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xp11.4

Genomic location:

Preferred name:

NM_001034853.2(RPGR):c.1217dup (p.Ser407fs)

HGVS:

NC_000023.11:g.38298984dup
NG_009553.1:g.33552dup
NM_000328.3:c.1217dup
NM_001034853.2:c.1217dupMANE SELECT
NM_001367245.1:c.1214dup
NM_001367246.1:c.1060-1532dup
NM_001367247.1:c.1217dup
NM_001367248.1:c.1247dup
NM_001367249.1:c.1214dup
NM_001367250.1:c.1214dup
NM_001367251.1:c.1060-1532dup
NP_000319.1:p.Ser407fs
NP_001030025.1:p.Ser407fs
NP_001354174.1:p.Ser406fs
NP_001354176.1:p.Ser407fs
NP_001354177.1:p.Ser417fs
NP_001354178.1:p.Ser406fs
NP_001354179.1:p.Ser406fs
NC_000023.10:g.38158236_38158237insA
NC_000023.10:g.38158237dup
NM_001034853.1:c.1217dup
NM_001034853.1:c.1217dupT
NR_159803.1:n.1419dup
NR_159804.1:n.1268dup
NR_159805.1:n.1359dup
NR_159806.1:n.1359dup
NR_159807.1:n.1359dup
NR_159808.1:n.1471dup

Protein change:

S406fs

Links:

dbSNP: rs1601943325

NCBI 1000 Genomes Browser:

rs1601943325

Molecular consequence:

NM_000328.3:c.1217dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001034853.2:c.1217dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367245.1:c.1214dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367247.1:c.1217dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367248.1:c.1247dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367249.1:c.1214dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367250.1:c.1214dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001367246.1:c.1060-1532dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001367251.1:c.1060-1532dup - intron variant - [Sequence Ontology: SO:0001627]
NR_159803.1:n.1419dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159804.1:n.1268dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159805.1:n.1359dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159806.1:n.1359dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159807.1:n.1359dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159808.1:n.1471dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168339	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 13, 2023)	germline	clinical testing	Citation Link,
SCV001249286	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jun 1, 2018)	germline	clinical testing	Citation Link,
SCV002759594	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 13, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168339

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jun 13, 2023)

germline

clinical testing

Citation Link,

SCV001249286

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jun 1, 2018)

germline

clinical testing

Citation Link,

SCV002759594

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 13, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV001168339.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28863407)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001249286.20

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV002759594.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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